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annotate scripts/spades.pl @ 2:6837f733b4aa draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 09:10:12 -0500
parents 965517909457
children
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1 #!/usr/bin/env perl
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2 ## A wrapper script to call spades.py and collect its output
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3 use strict;
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4 use warnings;
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5 use File::Temp qw/ tempfile tempdir /;
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6 use File::Copy;
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7 use Getopt::Long;
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8
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9 # Parse arguments
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10 my ($out_contigs_file,
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11 $out_contigs_stats,
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12 $out_scaffolds_file,
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13 $out_scaffolds_stats,
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14 $out_log_file,
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15 $new_name,
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16 @sysargs) = @ARGV;
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17
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18 ## GetOptions not compatible with parsing the rest of the arguments in an array.
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19 ## Keeping the not-so-nice parse-in-one-go method, without named arguments.
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20 # GetOptions(
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21 # 'contigs-file=s' => \$out_contigs_file,
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22 # 'contigs-stats=s' => \$out_contigs_stats,
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23 # 'scaffolds-file=s' => \$out_scaffolds_file,
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24 # 'scaffolds-stats=s' => \$out_scaffolds_stats,
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25 # 'out_log_file=s' => \$out_log_file,
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26 # );
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27
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28 # my @sysargs = @ARGV;
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29
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30 # Create temporary folder to store files, delete after use
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31 #my $output_dir = tempdir( CLEANUP => 0 );
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32 my $output_dir = 'output_dir';
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33 # Link "dat" files as fastq, otherwise spades complains about file format
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34
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35 # Create log handle
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36 open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
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37
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38 # Run program
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39 # To do: record time
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40 runSpades(@sysargs);
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41 collectOutput($new_name);
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42 extractCoverageLength($out_contigs_file, $out_contigs_stats);
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43 extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats);
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44 print $log "Done\n";
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45 close $log;
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46 exit 0;
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47
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48 # Run spades
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49 sub runSpades {
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50 my $cmd = join(" ", @_) . " -o $output_dir";
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51 my $return_code = system($cmd);
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52 if ($return_code) {
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53 print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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54 die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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55 }
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56 return 0;
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57 }
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58
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59 # Collect output
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60 sub collectOutput{
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61 my ($new_name) = @_;
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62
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63 # Collects output
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64 #if a new name is given for the contigs and scaffolds, change them before moving them
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65 if ( $new_name ne 'NODE') {
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66 renameContigs($new_name);
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67 }
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68 else {
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69 if ( -e "$output_dir/contigs.fasta") {
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70 move "$output_dir/contigs.fasta", $out_contigs_file;
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71 }
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72 if ( -e "$output_dir/scaffolds.fasta") {
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73 move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
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74 }
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75 }
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76
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77 open LOG, '<', "$output_dir/spades.log"
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78 or die "Cannot open log file $output_dir/spades.log: $?";
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79 print $log $_ while (<LOG>);
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80 return 0;
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81 }
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82
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83 #Change name in contig and scaffolds file
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84 sub renameContigs{
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85 my ($name) = @_;
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86
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87 open my $in, '<',"$output_dir/contigs.fasta" or die $!;
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88 open my $out,'>', $out_contigs_file;
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89
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90 while ( my $line = <$in>) {
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91 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
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92 #also move the remainder of the length
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93 if ( $line =~ />NODE_(\d+)_(.+)/) {
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94 $line = ">$name" . "_$1 $2\n";
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95 }
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96 print $out $line;
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97 }
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98 close $in;
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99 close $out;
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100
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101
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102 open $in, '<',"$output_dir/scaffolds.fasta" or die $!;
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103 open $out,'>', $out_scaffolds_file;
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104
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105 while ( my $line = <$in>) {
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106 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
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107 #also move the remainder of the length
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108 if ( $line =~ />NODE_(\d+)_(.+)/) {
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109 $line = ">$name" . "_$1 $2\n";
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110 }
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111 print $out $line;
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112 }
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113 close $in;
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114 close $out;
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115
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116 }
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117
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118
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119 # Extract
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120 sub extractCoverageLength{
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121 my ($in, $out) = @_;
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122 open FASTA, '<', $in or die $!;
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123 open TAB, '>', $out or die $!;
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124 print TAB "#name\tlength\tcoverage\n";
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125 while (<FASTA>){
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126 next unless /^>/;
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127 chomp;
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128 die "Not all elements found in $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/);
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129 my ($name,$n, $l, $cov) = ($1,$2, $3, $4);
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130 print TAB "$name" . "_$n\t$l\t$cov\n";
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131 }
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132 close TAB;
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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133 }